Variant report

Variant	rs828052
Chromosome Location	chr1:97608892-97608893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10430074	1.00[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs10875054	1.00[ASN][1000 genomes]
rs10875055	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs12063966	0.82[YRI][hapmap]
rs12066847	0.82[YRI][hapmap]
rs12127420	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12133667	1.00[CHB][hapmap]
rs1413227	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs1413229	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs1413231	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1413235	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs17471125	1.00[CHB][hapmap]
rs1970142	1.00[ASN][1000 genomes]
rs28619552	1.00[ASN][1000 genomes]
rs3762412	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs494271	1.00[CHB][hapmap]
rs4949945	1.00[ASN][1000 genomes]
rs4950023	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[ASN][1000 genomes]
rs496179	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs533365	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs595937	1.00[ASN][1000 genomes]
rs6593632	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs6593635	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6593636	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs6593637	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs6661442	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6673282	1.00[ASN][1000 genomes]
rs6681752	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs6683351	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs6683883	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs6692424	1.00[ASN][1000 genomes]
rs6693034	1.00[ASN][1000 genomes]
rs6697132	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs6700957	1.00[ASN][1000 genomes]
rs67665424	1.00[ASN][1000 genomes]
rs688913	1.00[ASN][1000 genomes]
rs7513333	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs7528359	1.00[ASN][1000 genomes]
rs7531100	1.00[ASN][1000 genomes]
rs7537668	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs7545506	1.00[ASN][1000 genomes]
rs828054	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828058	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs885622	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs914959	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830692	chr1:97501492-97625153	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97563600-97619200	Weak transcription	Dnd41	blood
2	chr1:97564200-97632800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:97585600-97621800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:97597400-97619600	Weak transcription	Liver	Liver
5	chr1:97603400-97610200	Weak transcription	Brain Germinal Matrix	brain
6	chr1:97604000-97610000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr1:97604000-97620000	Weak transcription	Pancreas	Pancrea
8	chr1:97604200-97610400	Weak transcription	Fetal Brain Male	brain
9	chr1:97604400-97609200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:97604400-97609600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:97604400-97611000	Weak transcription	Stomach Mucosa	stomach
12	chr1:97604400-97614800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:97604400-97629000	Weak transcription	Primary B cells from cord blood	blood
14	chr1:97604600-97609000	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:97604600-97609000	Weak transcription	NHLF	lung
16	chr1:97604600-97609400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:97604600-97609400	Weak transcription	A549	lung
18	chr1:97604600-97609400	Weak transcription	HUVEC	blood vessel
19	chr1:97604600-97609600	Weak transcription	HSMMtube	muscle
20	chr1:97604600-97609800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:97604600-97609800	Weak transcription	Brain Angular Gyrus	brain
22	chr1:97604600-97610200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:97604600-97614000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:97604800-97609200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:97605200-97609000	Weak transcription	HSMM	muscle
26	chr1:97605400-97609000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:97605600-97609000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:97606200-97610200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:97606200-97626600	Weak transcription	Ovary	ovary
30	chr1:97606800-97610400	Weak transcription	Primary T cells from cord blood	blood
31	chr1:97606800-97610400	Weak transcription	Aorta	Aorta
32	chr1:97607200-97611000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr1:97607400-97612600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:97608000-97609600	Enhancers	NH-A	brain
35	chr1:97608000-97610200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr1:97608200-97609000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:97608200-97609400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:97608600-97610200	Enhancers	Brain Substantia Nigra	brain
39	chr1:97608800-97609000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr1:97608800-97609200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:97608800-97610400	Enhancers	Osteobl	bone
42	chr1:97608800-97611200	Enhancers	NHEK	skin
43	chr1:97608800-97611400	Enhancers	Hela-S3	cervix
44	chr1:97608800-97611600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:97608800-97612000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:97608800-97612000	Enhancers	HMEC	breast
47	chr1:97608800-97612200	Enhancers	Brain Anterior Caudate	brain
48	chr1:97608800-97612200	Enhancers	NHDF-Ad	bronchial
49	chr1:97608800-97612400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links